I mean why would you be fully against flatpak? I use NixOS without it and always packaged natively on Arch, but especially when upstream offers flatpak, it makes sense to enable it. Keeps the user-facing programs up to date and somewhat sandboxed while you can have a stable release beneath it. Especially if the system's actual users aren't that tech-savvy.
Stuff on unstable tends to break, especially electron-dependent derivations. Stable doesn't always have the latest and greatest. Flatpak seems like a good compromise for desktop applications in some cases.
They're not that different from the classic nix files. Their main difference is that their inputs are always well-defined (as opposed to a channels registry, i.e. you can get totally different systems by reapplying a configuration when you change channels which doesn't change your nix file at all). A configuration is always exactly described by a flake.nix and flake.lock.
I mean there is more to it, but this is the primary motivation. What you would normally put into use case specific nix files goes into a flake's output section. The stuff in your input sections is what you can use in there.